limma and 2-array divided probe sets
1
0
Entering edit mode
@jorrit-boekel-1993
Last seen 9.6 years ago
Dear list, I would like to do an analysis on a published dataset that used the "previous generation" (quote Affy) arrays Mu11K. These contain ~11K probes divided over 2 chips, give rise to 2 cel files, and use different annotation packages. As I am no limma-veteran, I wondered if there was a way to concatenate the data from these files before or after reading it into limma as two separate affybatch objects, and then make an eSet. If not, should I instead analyse the chips separately and merge the resulting toptables? cheers, -- Jorrit Boekel Ph.D. student Dept. of Neuroscience Karolinska Institute Stockholm, Sweden
limma limma • 731 views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Jorrit Boekel ha scritto: > Dear list, > > I would like to do an analysis on a published dataset that used the > "previous generation" (quote Affy) arrays Mu11K. These contain ~11K > probes divided over 2 chips, give rise to 2 cel files, and use different > annotation packages. > > As I am no limma-veteran, I wondered if there was a way to concatenate > the data from these files before or after reading it into limma as two > separate affybatch objects, and then make an eSet. If not, should I > instead analyse the chips separately and merge the resulting toptables? > > cheers, Dear Jorrit it is better to do the normalisation and quality control separately. For whether you then merge pre or post differential expression analysis with limma, I don't see any big concerns either way, that is probably more a question of what you find more convenient. Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber
ADD COMMENT

Login before adding your answer.

Traffic: 718 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6